PDB-5cx7: Crystal Structure of PduOC:Heme Complex

基本情報

• 登録情報: データベース: PDB / ID: 5cx7
• タイトル: Crystal Structure of PduOC:Heme Complex
• 要素: ATP:cob(I)alamin adenosyltransferase
• キーワード: UNKNOWN FUNCTION / Bis-His / Heme binding domain / PduOC

機能・相同性

分子機能:

propanediol degradation polyhedral organelle / 1,2-propanediol catabolic process / corrinoid adenosyltransferase activity / 転移酵素; メチル基以外のアルキル基またはアリル基を移すもの; - / cobalamin biosynthetic process / ATP binding / metal ion binding

ドメイン・相同性:

Corrinoid adenosyltransferase PduO / Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta

構成要素:

PROTOPORPHYRIN IX CONTAINING FE / : / Corrinoid adenosyltransferase PduO

• 生物種: Salmonella enterica subsp. enterica serovar Livingstone (サルモネラ菌)
• 手法: X線回折 / シンクロトロン / 分子置換 / 解像度: 1.97 Å
• データ登録者: Geremia, S. / Hickey, N. / Ortiz de Orue Lucana, D.
• 引用: ジャーナル: Front Microbiol / 年: 2016; タイトル: The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode.; 著者: Ortiz de Orue Lucana, D. / Hickey, N. / Hensel, M. / Klare, J.P. / Geremia, S. / Tiufiakova, T. / Torda, A.E.

履歴

登録	2015年7月28日	登録サイト: RCSB / 処理サイト: PDBE
改定 1.0	2016年6月29日	Provider: repository / タイプ: Initial release
改定 1.1	2016年8月3日	Group: Database references
改定 1.2	2016年11月23日	Group: Derived calculations
改定 1.3	2024年1月10日	Group: Data collection / Database references / Derived calculations / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

集合体

登録構造単位

A: ATP:cob(I)alamin adenosyltransferase

B: ATP:cob(I)alamin adenosyltransferase

C: ATP:cob(I)alamin adenosyltransferase

D: ATP:cob(I)alamin adenosyltransferase

E: ATP:cob(I)alamin adenosyltransferase

F: ATP:cob(I)alamin adenosyltransferase

G: ATP:cob(I)alamin adenosyltransferase

H: ATP:cob(I)alamin adenosyltransferase

I: ATP:cob(I)alamin adenosyltransferase

J: ATP:cob(I)alamin adenosyltransferase

K: ATP:cob(I)alamin adenosyltransferase

L: ATP:cob(I)alamin adenosyltransferase

M: ATP:cob(I)alamin adenosyltransferase

N: ATP:cob(I)alamin adenosyltransferase

O: ATP:cob(I)alamin adenosyltransferase

P: ATP:cob(I)alamin adenosyltransferase

ヘテロ分子

概要:

• 255 kDa, 16 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	254,839	73
ポリマ－	247,001	16
非ポリマー	7,838	57
水	25,960	1441

1

A: ATP:cob(I)alamin adenosyltransferase

B: ATP:cob(I)alamin adenosyltransferase

C: ATP:cob(I)alamin adenosyltransferase

D: ATP:cob(I)alamin adenosyltransferase

E: ATP:cob(I)alamin adenosyltransferase

F: ATP:cob(I)alamin adenosyltransferase

G: ATP:cob(I)alamin adenosyltransferase

H: ATP:cob(I)alamin adenosyltransferase

ヘテロ分子

概要:

• 登録者・ソフトウェアが定義した集合体
• 127 kDa, 8 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	127,466	37
ポリマ－	123,500	8
非ポリマー	3,965	29
水	144	8

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

計算値:

Buried area	25430 Å2
ΔGint	-194 kcal/mol
Surface area	36640 Å2
手法	PISA

2

I: ATP:cob(I)alamin adenosyltransferase

J: ATP:cob(I)alamin adenosyltransferase

K: ATP:cob(I)alamin adenosyltransferase

L: ATP:cob(I)alamin adenosyltransferase

M: ATP:cob(I)alamin adenosyltransferase

N: ATP:cob(I)alamin adenosyltransferase

O: ATP:cob(I)alamin adenosyltransferase

P: ATP:cob(I)alamin adenosyltransferase

ヘテロ分子

概要:

• 登録者・ソフトウェアが定義した集合体
• 127 kDa, 8 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	127,374	36
ポリマ－	123,500	8
非ポリマー	3,873	28
水	144	8

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

計算値:

Buried area	24980 Å2
ΔGint	-195 kcal/mol
Surface area	36790 Å2
手法	PISA

単位格子

Length a, b, c (Å)	71.300, 130.120, 120.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	4
Space group name H-M	P1211

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID	詳細
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	A
2	12	M
1	13	A
2	13	N
1	14	A
2	14	O
1	15	A
2	15	P
1	16	B
2	16	C
1	17	B
2	17	D
1	18	B
2	18	E
1	19	B
2	19	F
1	20	B
2	20	G
1	21	B
2	21	H
1	22	B
2	22	I
1	23	B
2	23	J
1	24	B
2	24	K
1	25	B
2	25	L
1	26	B
2	26	M
1	27	B
2	27	N
1	28	B
2	28	O
1	29	B
2	29	P
1	30	C
2	30	D
1	31	C
2	31	E
1	32	C
2	32	F
1	33	C
2	33	G
1	34	C
2	34	H
1	35	C
2	35	I
1	36	C
2	36	J
1	37	C
2	37	K
1	38	C
2	38	L
1	39	C
2	39	M
1	40	C
2	40	N
1	41	C
2	41	O
1	42	C
2	42	P
1	43	D
2	43	E
1	44	D
2	44	F
1	45	D
2	45	G
1	46	D
2	46	H
1	47	D
2	47	I
1	48	D
2	48	J
1	49	D
2	49	K
1	50	D
2	50	L
1	51	D
2	51	M
1	52	D
2	52	N
1	53	D
2	53	O
1	54	D
2	54	P
1	55	E
2	55	F
1	56	E
2	56	G
1	57	E
2	57	H
1	58	E
2	58	I
1	59	E
2	59	J
1	60	E
2	60	K
1	61	E
2	61	L
1	62	E
2	62	M
1	63	E
2	63	N
1	64	E
2	64	O
1	65	E
2	65	P
1	66	F
2	66	G
1	67	F
2	67	H
1	68	F
2	68	I
1	69	F
2	69	J
1	70	F
2	70	K
1	71	F
2	71	L
1	72	F
2	72	M
1	73	F
2	73	N
1	74	F
2	74	O
1	75	F
2	75	P
1	76	G
2	76	H
1	77	G
2	77	I
1	78	G
2	78	J
1	79	G
2	79	K
1	80	G
2	80	L
1	81	G
2	81	M
1	82	G
2	82	N
1	83	G
2	83	O
1	84	G
2	84	P
1	85	H
2	85	I
1	86	H
2	86	J
1	87	H
2	87	K
1	88	H
2	88	L
1	89	H
2	89	M
1	90	H
2	90	N
1	91	H
2	91	O
1	92	H
2	92	P
1	93	I
2	93	J
1	94	I
2	94	K
1	95	I
2	95	L
1	96	I
2	96	M
1	97	I
2	97	N
1	98	I
2	98	O
1	99	I
2	99	P
1	100	J
2	100	K
1	101	J
2	101	L
1	102	J
2	102	M
1	103	J
2	103	N
1	104	J
2	104	O
1	105	J
2	105	P
1	106	K
2	106	L
1	107	K
2	107	M
1	108	K
2	108	N
1	109	K
2	109	O
1	110	K
2	110	P
1	111	L
2	111	M
1	112	L
2	112	N
1	113	L
2	113	O
1	114	L
2	114	P
1	115	M
2	115	N
1	116	M
2	116	O
1	117	M
2	117	P
1	118	N
2	118	O
1	119	N
2	119	P
1	120	O
2	120	P

NCSドメイン領域:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	A	A	10 - 147	10 - 147
2	1	GLN	GLN	B	B	10 - 147	10 - 147
1	2	GLN	GLN	A	A	10 - 147	10 - 147
2	2	GLN	GLN	C	C	10 - 147	10 - 147
1	3	GLN	GLN	A	A	10 - 147	10 - 147
2	3	GLN	GLN	D	D	10 - 147	10 - 147
1	4	HIS	HIS	A	A	10 - 146	10 - 146
2	4	HIS	HIS	E	E	10 - 146	10 - 146
1	5	GLN	GLN	A	A	10 - 147	10 - 147
2	5	GLN	GLN	F	F	10 - 147	10 - 147
1	6	GLN	GLN	A	A	10 - 147	10 - 147
2	6	GLN	GLN	G	G	10 - 147	10 - 147
1	7	GLN	GLN	A	A	10 - 147	10 - 147
2	7	GLN	GLN	H	H	10 - 147	10 - 147
1	8	GLN	GLN	A	A	10 - 147	10 - 147
2	8	GLN	GLN	I	I	10 - 147	10 - 147
1	9	GLN	GLN	A	A	10 - 147	10 - 147
2	9	GLN	GLN	J	J	10 - 147	10 - 147
1	10	GLN	GLN	A	A	10 - 147	10 - 147
2	10	GLN	GLN	K	K	10 - 147	10 - 147
1	11	GLN	GLN	A	A	10 - 147	10 - 147
2	11	GLN	GLN	L	L	10 - 147	10 - 147
1	12	GLN	GLN	A	A	10 - 147	10 - 147
2	12	GLN	GLN	M	M	10 - 147	10 - 147
1	13	GLN	GLN	A	A	10 - 147	10 - 147
2	13	GLN	GLN	N	N	10 - 147	10 - 147
1	14	GLN	GLN	A	A	10 - 147	10 - 147
2	14	GLN	GLN	O	O	10 - 147	10 - 147
1	15	GLN	GLN	A	A	10 - 147	10 - 147
2	15	GLN	GLN	P	P	10 - 147	10 - 147
1	16	GLN	GLN	B	B	10 - 147	10 - 147
2	16	GLN	GLN	C	C	10 - 147	10 - 147
1	17	GLN	GLN	B	B	10 - 147	10 - 147
2	17	GLN	GLN	D	D	10 - 147	10 - 147
1	18	HIS	HIS	B	B	10 - 146	10 - 146
2	18	HIS	HIS	E	E	10 - 146	10 - 146
1	19	GLN	GLN	B	B	10 - 147	10 - 147
2	19	GLN	GLN	F	F	10 - 147	10 - 147
1	20	GLN	GLN	B	B	10 - 147	10 - 147
2	20	GLN	GLN	G	G	10 - 147	10 - 147
1	21	GLN	GLN	B	B	10 - 147	10 - 147
2	21	GLN	GLN	H	H	10 - 147	10 - 147
1	22	GLN	GLN	B	B	10 - 147	10 - 147
2	22	GLN	GLN	I	I	10 - 147	10 - 147
1	23	GLN	GLN	B	B	10 - 147	10 - 147
2	23	GLN	GLN	J	J	10 - 147	10 - 147
1	24	GLN	GLN	B	B	10 - 147	10 - 147
2	24	GLN	GLN	K	K	10 - 147	10 - 147
1	25	GLN	GLN	B	B	10 - 147	10 - 147
2	25	GLN	GLN	L	L	10 - 147	10 - 147
1	26	GLN	GLN	B	B	10 - 147	10 - 147
2	26	GLN	GLN	M	M	10 - 147	10 - 147
1	27	GLN	GLN	B	B	10 - 147	10 - 147
2	27	GLN	GLN	N	N	10 - 147	10 - 147
1	28	GLN	GLN	B	B	10 - 147	10 - 147
2	28	GLN	GLN	O	O	10 - 147	10 - 147
1	29	GLN	GLN	B	B	10 - 147	10 - 147
2	29	GLN	GLN	P	P	10 - 147	10 - 147
1	30	GLN	GLN	C	C	10 - 147	10 - 147
2	30	GLN	GLN	D	D	10 - 147	10 - 147
1	31	HIS	HIS	C	C	10 - 146	10 - 146
2	31	HIS	HIS	E	E	10 - 146	10 - 146
1	32	GLN	GLN	C	C	10 - 147	10 - 147
2	32	GLN	GLN	F	F	10 - 147	10 - 147
1	33	GLN	GLN	C	C	10 - 147	10 - 147
2	33	GLN	GLN	G	G	10 - 147	10 - 147
1	34	GLN	GLN	C	C	10 - 147	10 - 147
2	34	GLN	GLN	H	H	10 - 147	10 - 147
1	35	GLN	GLN	C	C	10 - 147	10 - 147
2	35	GLN	GLN	I	I	10 - 147	10 - 147
1	36	GLN	GLN	C	C	10 - 147	10 - 147
2	36	GLN	GLN	J	J	10 - 147	10 - 147
1	37	GLN	GLN	C	C	10 - 147	10 - 147
2	37	GLN	GLN	K	K	10 - 147	10 - 147
1	38	GLN	GLN	C	C	10 - 147	10 - 147
2	38	GLN	GLN	L	L	10 - 147	10 - 147
1	39	GLN	GLN	C	C	10 - 147	10 - 147
2	39	GLN	GLN	M	M	10 - 147	10 - 147
1	40	GLN	GLN	C	C	10 - 147	10 - 147
2	40	GLN	GLN	N	N	10 - 147	10 - 147
1	41	GLN	GLN	C	C	10 - 147	10 - 147
2	41	GLN	GLN	O	O	10 - 147	10 - 147
1	42	GLN	GLN	C	C	10 - 147	10 - 147
2	42	GLN	GLN	P	P	10 - 147	10 - 147
1	43	HIS	HIS	D	D	10 - 146	10 - 146
2	43	HIS	HIS	E	E	10 - 146	10 - 146
1	44	GLN	GLN	D	D	10 - 147	10 - 147
2	44	GLN	GLN	F	F	10 - 147	10 - 147
1	45	GLN	GLN	D	D	10 - 147	10 - 147
2	45	GLN	GLN	G	G	10 - 147	10 - 147
1	46	GLN	GLN	D	D	10 - 147	10 - 147
2	46	GLN	GLN	H	H	10 - 147	10 - 147
1	47	GLN	GLN	D	D	10 - 147	10 - 147
2	47	GLN	GLN	I	I	10 - 147	10 - 147
1	48	GLN	GLN	D	D	10 - 147	10 - 147
2	48	GLN	GLN	J	J	10 - 147	10 - 147
1	49	GLN	GLN	D	D	10 - 147	10 - 147
2	49	GLN	GLN	K	K	10 - 147	10 - 147
1	50	GLN	GLN	D	D	10 - 147	10 - 147
2	50	GLN	GLN	L	L	10 - 147	10 - 147
1	51	GLN	GLN	D	D	10 - 147	10 - 147
2	51	GLN	GLN	M	M	10 - 147	10 - 147
1	52	GLN	GLN	D	D	10 - 147	10 - 147
2	52	GLN	GLN	N	N	10 - 147	10 - 147
1	53	GLN	GLN	D	D	10 - 147	10 - 147
2	53	GLN	GLN	O	O	10 - 147	10 - 147
1	54	GLN	GLN	D	D	10 - 147	10 - 147
2	54	GLN	GLN	P	P	10 - 147	10 - 147
1	55	HIS	HIS	E	E	10 - 146	10 - 146
2	55	HIS	HIS	F	F	10 - 146	10 - 146
1	56	HIS	HIS	E	E	10 - 146	10 - 146
2	56	HIS	HIS	G	G	10 - 146	10 - 146
1	57	HIS	HIS	E	E	10 - 146	10 - 146
2	57	HIS	HIS	H	H	10 - 146	10 - 146
1	58	HIS	HIS	E	E	10 - 146	10 - 146
2	58	HIS	HIS	I	I	10 - 146	10 - 146
1	59	HIS	HIS	E	E	10 - 146	10 - 146
2	59	HIS	HIS	J	J	10 - 146	10 - 146
1	60	HIS	HIS	E	E	10 - 146	10 - 146
2	60	HIS	HIS	K	K	10 - 146	10 - 146
1	61	HIS	HIS	E	E	10 - 146	10 - 146
2	61	HIS	HIS	L	L	10 - 146	10 - 146
1	62	HIS	HIS	E	E	10 - 146	10 - 146
2	62	HIS	HIS	M	M	10 - 146	10 - 146
1	63	HIS	HIS	E	E	10 - 146	10 - 146
2	63	HIS	HIS	N	N	10 - 146	10 - 146
1	64	HIS	HIS	E	E	10 - 146	10 - 146
2	64	HIS	HIS	O	O	10 - 146	10 - 146
1	65	HIS	HIS	E	E	10 - 146	10 - 146
2	65	HIS	HIS	P	P	10 - 146	10 - 146
1	66	GLN	GLN	F	F	10 - 147	10 - 147
2	66	GLN	GLN	G	G	10 - 147	10 - 147
1	67	GLN	GLN	F	F	10 - 147	10 - 147
2	67	GLN	GLN	H	H	10 - 147	10 - 147
1	68	GLN	GLN	F	F	10 - 147	10 - 147
2	68	GLN	GLN	I	I	10 - 147	10 - 147
1	69	GLN	GLN	F	F	10 - 147	10 - 147
2	69	GLN	GLN	J	J	10 - 147	10 - 147
1	70	GLN	GLN	F	F	10 - 147	10 - 147
2	70	GLN	GLN	K	K	10 - 147	10 - 147
1	71	GLN	GLN	F	F	10 - 147	10 - 147
2	71	GLN	GLN	L	L	10 - 147	10 - 147
1	72	GLN	GLN	F	F	10 - 147	10 - 147
2	72	GLN	GLN	M	M	10 - 147	10 - 147
1	73	GLN	GLN	F	F	10 - 147	10 - 147
2	73	GLN	GLN	N	N	10 - 147	10 - 147
1	74	GLN	GLN	F	F	10 - 147	10 - 147
2	74	GLN	GLN	O	O	10 - 147	10 - 147
1	75	GLN	GLN	F	F	10 - 147	10 - 147
2	75	GLN	GLN	P	P	10 - 147	10 - 147
1	76	GLN	GLN	G	G	10 - 147	10 - 147
2	76	GLN	GLN	H	H	10 - 147	10 - 147
1	77	GLN	GLN	G	G	10 - 147	10 - 147
2	77	GLN	GLN	I	I	10 - 147	10 - 147
1	78	GLN	GLN	G	G	10 - 147	10 - 147
2	78	GLN	GLN	J	J	10 - 147	10 - 147
1	79	GLN	GLN	G	G	10 - 147	10 - 147
2	79	GLN	GLN	K	K	10 - 147	10 - 147
1	80	GLN	GLN	G	G	10 - 147	10 - 147
2	80	GLN	GLN	L	L	10 - 147	10 - 147
1	81	GLN	GLN	G	G	10 - 147	10 - 147
2	81	GLN	GLN	M	M	10 - 147	10 - 147
1	82	GLN	GLN	G	G	10 - 147	10 - 147
2	82	GLN	GLN	N	N	10 - 147	10 - 147
1	83	GLN	GLN	G	G	10 - 147	10 - 147
2	83	GLN	GLN	O	O	10 - 147	10 - 147
1	84	GLN	GLN	G	G	10 - 147	10 - 147
2	84	GLN	GLN	P	P	10 - 147	10 - 147
1	85	GLN	GLN	H	H	10 - 147	10 - 147
2	85	GLN	GLN	I	I	10 - 147	10 - 147
1	86	GLN	GLN	H	H	10 - 147	10 - 147
2	86	GLN	GLN	J	J	10 - 147	10 - 147
1	87	GLN	GLN	H	H	10 - 147	10 - 147
2	87	GLN	GLN	K	K	10 - 147	10 - 147
1	88	GLN	GLN	H	H	10 - 147	10 - 147
2	88	GLN	GLN	L	L	10 - 147	10 - 147
1	89	GLN	GLN	H	H	10 - 147	10 - 147
2	89	GLN	GLN	M	M	10 - 147	10 - 147
1	90	GLN	GLN	H	H	10 - 147	10 - 147
2	90	GLN	GLN	N	N	10 - 147	10 - 147
1	91	GLN	GLN	H	H	10 - 147	10 - 147
2	91	GLN	GLN	O	O	10 - 147	10 - 147
1	92	GLN	GLN	H	H	10 - 147	10 - 147
2	92	GLN	GLN	P	P	10 - 147	10 - 147
1	93	GLN	GLN	I	I	10 - 147	10 - 147
2	93	GLN	GLN	J	J	10 - 147	10 - 147
1	94	GLN	GLN	I	I	10 - 147	10 - 147
2	94	GLN	GLN	K	K	10 - 147	10 - 147
1	95	GLN	GLN	I	I	10 - 147	10 - 147
2	95	GLN	GLN	L	L	10 - 147	10 - 147
1	96	GLN	GLN	I	I	10 - 147	10 - 147
2	96	GLN	GLN	M	M	10 - 147	10 - 147
1	97	GLN	GLN	I	I	10 - 147	10 - 147
2	97	GLN	GLN	N	N	10 - 147	10 - 147
1	98	GLN	GLN	I	I	10 - 147	10 - 147
2	98	GLN	GLN	O	O	10 - 147	10 - 147
1	99	GLN	GLN	I	I	10 - 147	10 - 147
2	99	GLN	GLN	P	P	10 - 147	10 - 147
1	100	GLN	GLN	J	J	10 - 147	10 - 147
2	100	GLN	GLN	K	K	10 - 147	10 - 147
1	101	GLN	GLN	J	J	10 - 147	10 - 147
2	101	GLN	GLN	L	L	10 - 147	10 - 147
1	102	GLN	GLN	J	J	10 - 147	10 - 147
2	102	GLN	GLN	M	M	10 - 147	10 - 147
1	103	GLN	GLN	J	J	10 - 147	10 - 147
2	103	GLN	GLN	N	N	10 - 147	10 - 147
1	104	GLN	GLN	J	J	10 - 147	10 - 147
2	104	GLN	GLN	O	O	10 - 147	10 - 147
1	105	GLN	GLN	J	J	10 - 147	10 - 147
2	105	GLN	GLN	P	P	10 - 147	10 - 147
1	106	GLN	GLN	K	K	10 - 147	10 - 147
2	106	GLN	GLN	L	L	10 - 147	10 - 147
1	107	GLN	GLN	K	K	10 - 147	10 - 147
2	107	GLN	GLN	M	M	10 - 147	10 - 147
1	108	GLN	GLN	K	K	10 - 147	10 - 147
2	108	GLN	GLN	N	N	10 - 147	10 - 147
1	109	GLN	GLN	K	K	10 - 147	10 - 147
2	109	GLN	GLN	O	O	10 - 147	10 - 147
1	110	GLN	GLN	K	K	10 - 147	10 - 147
2	110	GLN	GLN	P	P	10 - 147	10 - 147
1	111	GLN	GLN	L	L	10 - 147	10 - 147
2	111	GLN	GLN	M	M	10 - 147	10 - 147
1	112	GLN	GLN	L	L	10 - 147	10 - 147
2	112	GLN	GLN	N	N	10 - 147	10 - 147
1	113	GLN	GLN	L	L	10 - 147	10 - 147
2	113	GLN	GLN	O	O	10 - 147	10 - 147
1	114	GLN	GLN	L	L	10 - 147	10 - 147
2	114	GLN	GLN	P	P	10 - 147	10 - 147
1	115	GLN	GLN	M	M	10 - 147	10 - 147
2	115	GLN	GLN	N	N	10 - 147	10 - 147
1	116	GLN	GLN	M	M	10 - 147	10 - 147
2	116	GLN	GLN	O	O	10 - 147	10 - 147
1	117	GLN	GLN	M	M	10 - 147	10 - 147
2	117	GLN	GLN	P	P	10 - 147	10 - 147
1	118	GLN	GLN	N	N	10 - 147	10 - 147
2	118	GLN	GLN	O	O	10 - 147	10 - 147
1	119	GLN	GLN	N	N	10 - 147	10 - 147
2	119	GLN	GLN	P	P	10 - 147	10 - 147
1	120	GLN	GLN	O	O	10 - 147	10 - 147
2	120	GLN	GLN	P	P	10 - 147	10 - 147

NCSアンサンブル:

ID
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8
9
10
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13
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16
17
18
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31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
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120

要素

タンパク質 , 1種, 16分子 A B C D E F G H I J K L M N O P

#1: タンパク質

A B C D E F G H I J K L M N O P
ATP:cob(I)alamin adenosyltransferase

詳細:

分子量: 15437.539 Da / 分子数: 16 / 由来タイプ: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Livingstone (サルモネラ菌)
遺伝子: VN13_17650 / プラスミド: pETPduO / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A0F0IPG3, UniProt: A0A1A9TAI7*PLUS

非ポリマー , 6種, 1498分子

#2: 化合物

A-201 C-201 E-201 G-201 I-201 K-201 M-201 O-201
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME

詳細:

分子量: 616.487 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C₃₄H₃₂FeN₄O₄

#3: 化合物

A-202 A-203 A-204 B-201 C-202 D-201 D-202 E-202 F-201 G-202 G-203 G-204 H-201 I-202 I-203 I-204 I-205 J-201 K-202 K-203 ...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

詳細:

分子量: 92.094 Da / 分子数: 25 / 由来タイプ: 合成 / 式: C₃H₈O₃

#4: 化合物

A-205 A-206 B-202 D-203 E-203 F-202 G-205 H-203 H-204 I-206 I-208 J-202 J-204 L-201 M-203 M-204 N-202 P-201
ChemComp-NA / SODIUM ION

詳細:

分子量: 22.990 Da / 分子数: 18 / 由来タイプ: 合成 / 式: Na

#5: 化合物

C-203 D-204 I-207 J-203
ChemComp-CL / CHLORIDE ION

詳細:

分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl

#6: 化合物

H-202 P-203 ChemComp-MG / MAGNESIUM ION

詳細:

分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg

#7: 水

ChemComp-HOH / water

詳細:

分子量: 18.015 Da / 分子数: 1441 / 由来タイプ: 天然 / 式: H₂O

実験情報

実験

• 実験: 手法: X線回折

試料調製

• 結晶: マシュー密度: 2.27 ų/Da / 溶媒含有率: 45.76 %
• 結晶化: 温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: PEG 3350 15% (w/v), 0.1 M magnesium formate

データ収集

• 回折: 平均測定温度: 100 K
• 放射光源: 由来: シンクロトロン / サイト: ELETTRA / ビームライン: 5.2R / 波長: 1 Å
• 検出器: タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2015年5月1日
• 放射: モノクロメーター: GRAPHITE / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
• 放射波長: 波長: 1 Å / 相対比: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.204
1	1	-h,-k,l	2	0.796

• 反射: 解像度: 1.97→33.07 Å / Num. obs: 152372 / % possible obs: 98.2 % / 冗長度: 2.64 % / R_merge(I) obs: 0.091 / Net I/σ(I): 7.8
• 反射 シェル: 解像度: 1.97→2.08 Å / 冗長度: 2.6 % / R_merge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / Num. unique all: 22309 / % possible all: 98.8

解析

ソフトウェア

名称	バージョン	分類
REFMAC	5.8.0103	精密化
MOSFLM		データ削減
SCALA		データスケーリング
AMoRE		位相決定

精密化

構造決定の手法: 分子置換
開始モデル: 2A2L

2a2l

解像度: 1.97→33.07 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.947 / SU B: 2.258 / SU ML: 0.068 / 交差検証法: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.028 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	反射数	%反射	Selection details
Rfree	0.18564	7771	5.1 %	RANDOM
Rwork	0.15803	-	-	-
obs	0.15943	144524	97.98 %	-

• 溶媒の処理: イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK

原子変位パラメータ

B_iso mean: 22.703 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-7.87 Å2	-0 Å2	1.52 Å2
2-	-	18.86 Å2	0 Å2
3-	-	-	-11 Å2

精密化ステップ

サイクル: 1 / 解像度: 1.97→33.07 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	16391	0	518	1441	18350

拘束条件

Refine-ID	タイプ	Dev ideal	Dev ideal target	数
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	17237
X-RAY DIFFRACTION	r_bond_other_d	0.016	0.02	16605
X-RAY DIFFRACTION	r_angle_refined_deg	1.998	1.98	23656
X-RAY DIFFRACTION	r_angle_other_deg	2.196	3	37967
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.861	5	2193
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.253	24.75	640
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.033	15	2624
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.957	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	2778
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	19751
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	3841
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.16	1.983	8820
X-RAY DIFFRACTION	r_mcbond_other	2.16	1.983	8819
X-RAY DIFFRACTION	r_mcangle_it	2.926	2.963	10997
X-RAY DIFFRACTION	r_mcangle_other	2.926	2.963	10998
X-RAY DIFFRACTION	r_scbond_it	3.241	2.442	8417
X-RAY DIFFRACTION	r_scbond_other	3.241	2.442	8417
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.741	3.554	12660
X-RAY DIFFRACTION	r_long_range_B_refined	6.879	18.395	20891
X-RAY DIFFRACTION	r_long_range_B_other	6.88	18.379	20880
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / タイプ: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	数	Rms dev position (Å)
1	1	A	16460	0.07
1	2	B	16460	0.07
2	1	A	16544	0.07
2	2	C	16544	0.07
3	1	A	16610	0.07
3	2	D	16610	0.07
4	1	A	16400	0.07
4	2	E	16400	0.07
5	1	A	16520	0.07
5	2	F	16520	0.07
6	1	A	16512	0.07
6	2	G	16512	0.07
7	1	A	16582	0.07
7	2	H	16582	0.07
8	1	A	16480	0.07
8	2	I	16480	0.07
9	1	A	16468	0.08
9	2	J	16468	0.08
10	1	A	16644	0.06
10	2	K	16644	0.06
11	1	A	16600	0.07
11	2	L	16600	0.07
12	1	A	16382	0.08
12	2	M	16382	0.08
13	1	A	16422	0.08
13	2	N	16422	0.08
14	1	A	16594	0.07
14	2	O	16594	0.07
15	1	A	16380	0.08
15	2	P	16380	0.08
16	1	B	16750	0.07
16	2	C	16750	0.07
17	1	B	16618	0.07
17	2	D	16618	0.07
18	1	B	16374	0.08
18	2	E	16374	0.08
19	1	B	16790	0.07
19	2	F	16790	0.07
20	1	B	16822	0.06
20	2	G	16822	0.06
21	1	B	16756	0.06
21	2	H	16756	0.06
22	1	B	16858	0.05
22	2	I	16858	0.05
23	1	B	16972	0.04
23	2	J	16972	0.04
24	1	B	16676	0.07
24	2	K	16676	0.07
25	1	B	16714	0.07
25	2	L	16714	0.07
26	1	B	16970	0.04
26	2	M	16970	0.04
27	1	B	16904	0.06
27	2	N	16904	0.06
28	1	B	16748	0.06
28	2	O	16748	0.06
29	1	B	16748	0.06
29	2	P	16748	0.06
30	1	C	16642	0.07
30	2	D	16642	0.07
31	1	C	16414	0.07
31	2	E	16414	0.07
32	1	C	16550	0.08
32	2	F	16550	0.08
33	1	C	16550	0.08
33	2	G	16550	0.08
34	1	C	16582	0.08
34	2	H	16582	0.08
35	1	C	16676	0.07
35	2	I	16676	0.07
36	1	C	16774	0.07
36	2	J	16774	0.07
37	1	C	16818	0.05
37	2	K	16818	0.05
38	1	C	16634	0.07
38	2	L	16634	0.07
39	1	C	16734	0.07
39	2	M	16734	0.07
40	1	C	16728	0.07
40	2	N	16728	0.07
41	1	C	16608	0.07
41	2	O	16608	0.07
42	1	C	16672	0.07
42	2	P	16672	0.07
43	1	D	16720	0.06
43	2	E	16720	0.06
44	1	D	16798	0.06
44	2	F	16798	0.06
45	1	D	16776	0.06
45	2	G	16776	0.06
46	1	D	16732	0.07
46	2	H	16732	0.07
47	1	D	16730	0.07
47	2	I	16730	0.07
48	1	D	16676	0.07
48	2	J	16676	0.07
49	1	D	16738	0.06
49	2	K	16738	0.06
50	1	D	16934	0.05
50	2	L	16934	0.05
51	1	D	16704	0.07
51	2	M	16704	0.07
52	1	D	16676	0.07
52	2	N	16676	0.07
53	1	D	16850	0.06
53	2	O	16850	0.06
54	1	D	16610	0.08
54	2	P	16610	0.08
55	1	E	16544	0.06
55	2	F	16544	0.06
56	1	E	16534	0.07
56	2	G	16534	0.07
57	1	E	16548	0.07
57	2	H	16548	0.07
58	1	E	16490	0.08
58	2	I	16490	0.08
59	1	E	16416	0.07
59	2	J	16416	0.07
60	1	E	16508	0.06
60	2	K	16508	0.06
61	1	E	16652	0.06
61	2	L	16652	0.06
62	1	E	16444	0.08
62	2	M	16444	0.08
63	1	E	16426	0.08
63	2	N	16426	0.08
64	1	E	16596	0.07
64	2	O	16596	0.07
65	1	E	16422	0.08
65	2	P	16422	0.08
66	1	F	16960	0.05
66	2	G	16960	0.05
67	1	F	16790	0.07
67	2	H	16790	0.07
68	1	F	16762	0.07
68	2	I	16762	0.07
69	1	F	16788	0.06
69	2	J	16788	0.06
70	1	F	16748	0.06
70	2	K	16748	0.06
71	1	F	16922	0.05
71	2	L	16922	0.05
72	1	F	16848	0.06
72	2	M	16848	0.06
73	1	F	16818	0.06
73	2	N	16818	0.06
74	1	F	16920	0.05
74	2	O	16920	0.05
75	1	F	16596	0.07
75	2	P	16596	0.07
76	1	G	16812	0.06
76	2	H	16812	0.06
77	1	G	16736	0.07
77	2	I	16736	0.07
78	1	G	16870	0.05
78	2	J	16870	0.05
79	1	G	16756	0.06
79	2	K	16756	0.06
80	1	G	16918	0.05
80	2	L	16918	0.05
81	1	G	16888	0.06
81	2	M	16888	0.06
82	1	G	16752	0.07
82	2	N	16752	0.07
83	1	G	16978	0.04
83	2	O	16978	0.04
84	1	G	16618	0.07
84	2	P	16618	0.07
85	1	H	16578	0.08
85	2	I	16578	0.08
86	1	H	16652	0.07
86	2	J	16652	0.07
87	1	H	16684	0.07
87	2	K	16684	0.07
88	1	H	16836	0.07
88	2	L	16836	0.07
89	1	H	16640	0.07
89	2	M	16640	0.07
90	1	H	16578	0.08
90	2	N	16578	0.08
91	1	H	16950	0.06
91	2	O	16950	0.06
92	1	H	16824	0.05
92	2	P	16824	0.05
93	1	I	16898	0.05
93	2	J	16898	0.05
94	1	I	16612	0.07
94	2	K	16612	0.07
95	1	I	16708	0.07
95	2	L	16708	0.07
96	1	I	16940	0.06
96	2	M	16940	0.06
97	1	I	16852	0.07
97	2	N	16852	0.07
98	1	I	16700	0.07
98	2	O	16700	0.07
99	1	I	16706	0.07
99	2	P	16706	0.07
100	1	J	16706	0.07
100	2	K	16706	0.07
101	1	J	16722	0.06
101	2	L	16722	0.06
102	1	J	16980	0.04
102	2	M	16980	0.04
103	1	J	16910	0.05
103	2	N	16910	0.05
104	1	J	16758	0.06
104	2	O	16758	0.06
105	1	J	16756	0.06
105	2	P	16756	0.06
106	1	K	16742	0.06
106	2	L	16742	0.06
107	1	K	16630	0.07
107	2	M	16630	0.07
108	1	K	16646	0.07
108	2	N	16646	0.07
109	1	K	16722	0.07
109	2	O	16722	0.07
110	1	K	16482	0.08
110	2	P	16482	0.08
111	1	L	16796	0.07
111	2	M	16796	0.07
112	1	L	16694	0.07
112	2	N	16694	0.07
113	1	L	16980	0.05
113	2	O	16980	0.05
114	1	L	16650	0.07
114	2	P	16650	0.07
115	1	M	16926	0.05
115	2	N	16926	0.05
116	1	M	16802	0.06
116	2	O	16802	0.06
117	1	M	16736	0.06
117	2	P	16736	0.06
118	1	N	16664	0.07
118	2	O	16664	0.07
119	1	N	16680	0.07
119	2	P	16680	0.07
120	1	O	16754	0.06
120	2	P	16754	0.06

LS精密化 シェル

解像度: 1.969→2.02 Å / Total num. of bins used: 20

	Rfactor	反射数	%反射
Rfree	0.235	616	-
Rwork	0.192	10633	-
obs	-	-	98.68 %